The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Automating the identification of DNA variations using quality-based fluorescence re-sequencing: analysis of the human mitochondrial genome
Open accessAbstract
Diagnostic re-sequencing plays a central role in medical and evolutionary genetics. In this report we describe a process that applies fluorescence-based re-sequencing and an integrated set of analysis tools to automate and simplify the identification of DNA variations using the human mitochondrial genome as a model system. Two programs used in genome sequence analysis (Phred, a base-caller, and Phrap, a sequence assembler) are applied to assess the quality of each base call across the sequence. Potential DNA variants are automatically identified and 'tagged' by comparing the assembled sequence with a reference sequence. We also show that employing the Consed program to display a set of highly annotated reference sequences greatly simplifies data analysis by providing a visual database containing information on the location of the PCR primers, coding and regulatory sequences and previously known DNA variants. Among the 12 genomes sequenced 378 variants including 29 new variants were identified along with two heteroplasmic sites, automatically detected by the PolyPhred program. Overall we document the ease and speed of performing high quality and accurate fluorescence-based re-sequencing on long tracts of DNA as well as the application of new approaches to automatically find and view DNA variants among these sequences.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Mitochondrial DNA and human evolution
Cann, R. L., Stoneking, M., & Wilson, A. C. (1987) · Nature · doi:10.1038/325031a0 · Cited by 3,100
Identification of the remains of the Romanov family by DNA analysis
Gill, P., Ivanov, P. L., Kimpton, C., Piercy, R., Benson, N., Tully, G., Evett, I., Hagelberg, E., & Sullivan, K. (1994) · Nature Genetics · doi:10.1038/ng0294-130 · Cited by 693
Ivanov, P. L., Wadhams, M. J., Roby, R. K., Holland, M. M., Weedn, V. W., & Parsons, T. J. (1996) · Nature Genetics · doi:10.1038/ng0496-417 · Cited by 348
Cited by
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
Chin, C.-S., Alexander, D. H., Marks, P., Klammer, A. A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E. E., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2474 · Cited by 4,029
Linkage Disequilibrium and Recombination in Hominid Mitochondrial DNA
Awadalla, P., Eyre-Walker, A., & Smith, J. M. (1999) · Science · doi:10.1126/science.286.5449.2524 · Cited by 337
Fagundes, N. J. R., Kanitz, R., Eckert, R., Valls, A. C. S., Bogo, M. R., Salzano, F. M., Smith, D. G., Silva, W. A., Zago, M. A., Ribeiro-dos-Santos, A. K., et al. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2007.11.013 · Cited by 264
Expanding Southwest Pacific mitochondrial haplogroups P and Q
Friedlaender, J., Schurr, T., Gentz, F., Koki, G., Friedlaender, F., Horvat, G., Babb, P., Cerchio, S., Kaestle, F., Schanfield, M., et al. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi142 · Cited by 107
Zhang, L., Rao, F., Zhang, K., Khandrika, S., Das, M., Vaingankar, S. M., Bao, X., Rana, B. K., Smith, D. W., Wessel, J., et al. (2007) · Journal of Clinical Investigation · doi:10.1172/jci31093 · Cited by 90
Metadata
- Authors
- Rieder, M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 1998-02-01
- Volume
- 26
- Issue
- 4
- Pages
- 967-973
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2162135801
- Cited by
- 506
- References
- 3
- FWCI
- 3.38
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Automating the identification of DNA variations using quality-based fluorescence re-sequencing: analysis of the human mitochondrial genome. https://app.cochat.ai/papers/10.1093/nar/26.4.967
- The paper
- Rieder, M. (1998). Automating the identification of DNA variations using quality-based fluorescence re-sequencing: analysis of the human mitochondrial genome. Nucleic Acids Research. https://doi.org/10.1093/nar/26.4.967
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
